I have custom plugin which registers multiple CPT's and i want to reuse the features of wp-posts-to-posts to define relationships. I'm just wondering what is the correct/best way to include the api.php file within my own plugin?

If the posts-to-posts plugin is running on your site, I am not sure you'd need to include api.php but of course that depends on how the plugin works making the question off-topic as dependent on third party code.
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s_ha_dum♦Oct 15 '14 at 20:00